Contents

September 2008 E-Phys Protocol

9/22/2008 Setup and Surgery
1. Identify potential electrodes with combined fMRI/CT
2. Create log file on log computer
4. Record resting activity to make sure system is working

Microelectrode array experiments
If the new electrodes are ready, it will be a top priority to investigate their properties. A good start will be to compare small electrode LFPs with nearby big electrode LFPs.

1. LFP selectivity

Are microelectrodes more selective within-category than large electrodes?

How does selectivity vary within a single microelectrode array (MEA)?

2. Response amplitude/latency/duration

--Within an object-selective visual area, do different patches of cortex depolarize at different latencies or durations?

--Probably not, but we may have to adjust the pre-amp or amplifier settings.

3. Receptive Field Size

• Do small electrodes have smaller RFs than big electrodes?

4. Gamma oscillation

• Are oscillations in the gamma band more correlated among nearby electrodes than far electrodes?

5. Adaptation

• Do microelectrodes demonstrate different adaptation behavior than large electrodes?

• Do different microelectrodes within an ME array adapt differently to the same repeated stimuli?

6. Choice probability

• Does the pattern of activity in object-selective cortical areas correlate in anyway with the subject's behavior?

B. Stimulation
If would be really interesting to compare perception thresholds. We might predict thresholds would be lower with small electrodes because of high current density.
If the RFs are more selective (#1 above) then we might evoke percept with a small electrodes (because we are stimulating neurons with similar selectivity) where we could not with a big electrode.

Processing Subject Data

After obtaining the CD containing the patient CT data from St. Luke's, use OsiriX to export all images
(using the export to DICOM option, and the hierarchical, uncompress options).

CT scans have voxel size 0.488x0.488x1 mm; this may need to be adjusted manually with

3drefit -zdel 1.000 DE_CTSDE+orig

(If the CTs look distorted in AFNI, then the voxel size must be adjusted).
Next, the CTs must be registered with the hi-res presurgical MRI anatomy.
This may fail because the CT has a coordinate system with a very different origin than the MRI.
Registration routines will not work if the input datasets are not in rough alignment.
To check this, type

Check in AFNI to make sure that they alignment is correct. NB: It is also possible to crop the MRI before Allineating since the MR coverage is typically greater than the CT coverage. In a test case, this did not have a big effect.

Things to do

HumanImageDetection

Can stimuli be vector-based rather than pixel based, so as not to lose resolution with scaling? POSSIBLE if original file is vector-based

Enable online scrambling LOOKING INTO IT

Enable online color to black and white conversion LOOKING INTO IT

HumanLetterDetection

Analyze data from LR to see where the RFs are

DEBUGGING KNOT PROBLEMS

First, quit Knot.
Then, unplug one ITC from the USB port, wait for the power light to go off, plug it back in.
Repeat this, one at a time, for all ITCs.
Before beginning experiment, always make sure you get nice traces in Channel Data window, not just flat lines (even if looks nice on oscilloscope).